Job ID 8520
The program can send the superimposed coordinates by e-mail if you give your
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 *=*=*=*=*=*=*=*=*=*=*=
  Program:  TOP --- Version 6.7 (Internet) Feb 2001
   Author:  Guoguang Lu, Ph.D
   Address: Department of Molecular Biophysics
            Lund University
            Box 124, 221 00, Lund, Sweden
   E-mail:  Guoguang.Lu@mbfys.lu.se
   ftp:     ftp://bioinfo1.mbfys.lu.se/pub/guoguang/top.tar.Z
   WWW:     http://bioinfo1.mbfys.lu.se/TOP
   Date:    Dec 1991, BMC, Uppsala, Sweden (V1,V2)
            Sep 1995, Purdue Univ, USA (V3,V4)
            Jul 1996, Karolinska Inst., Sweden (V5,V6)
            Sep 1999, Lund University (V6.5 for g77)
 *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=

Automatic mode of the program:
Least matching rate for the two molecules  0.31
Least second matching rate  0.90
 * Secondary structure assignment completed
  418 Ca atoms read    11 helixes   15 strands in file mol1.pdb
 TITLE     CRYSTAL STRUCTURE ANALYSIS OF THE TERNARY COMPLEX BETWEEN
 TITLE    2 PSYCHROPHILIC ALPHA AMYLASE FROM PSEUDOALTEROMONAS
 TITLE    3 HALOPLANCTIS IN COMPLEX WITH A HEPTA-SACCHARIDE AND A TRIS
 TITLE    4 MOLECULE
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: ALPHA-AMYLASE;
 COMPND   3 CHAIN: A;
 COMPND   4 SYNONYM: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE;
 COMPND   5 EC: 3.2.1.1
  455 Ca atoms read    20 helixes   23 strands in file mol2.pdb
 1 chains in Mol2 
 Chain A Nr 1 42
 ----------------------------------------------------------------------
  13 of ( 26, 42) secondary structure could be aligned.
 ---------------------------------------------------+-----+-----+------
  Nr.E  Mol1 start  endmatch Nr.E  Mol2 start  end !angle! dst ! r.m.s
 ---------------------------------------------------+-----+-----+------
   1-b:  11     4-    6 ====   1-b:  A1 A   5-A   8 ! 11.1!  0.5!  2.6
   2-a:   1    19-   24 .==.   2-a:   1 A  12-A  23 ! 14.0!  0.8!  6.8
   3-a:   2    27-   32 ====   3-a:   2 A  23-A  28 ! 12.1!  0.1!  3.5
   4-b:  22    37-   40 ====   4-b:  A2 A  31-A  34 !  5.8!  0.8!  1.0
   5-a:   3    68-   80 ====   6-a:   4 A  63-A  77 !  1.7!  0.7!  2.0
   6-b:  33    84-   89 ====   7-b:  A3 A  80-A  86 !  0.9!  0.4!  2.5
   7-b:  44    98-   99  ..    8-b:  B1 A  89-A  90 ! 97.9!  5.4! 14.7
   8-b:  55   105-  107  ..    8-b:  B1 A  89-A  90 ! 96.4!  9.0! 11.8
  10-b:  66   176-  179 ====  16-b:  A4 A 170-A 174 !  8.7!  0.2!  2.1
  11-a:   5   187-  197 ====  18-a:  10 A 180-A 190 !  6.3!  1.1!  3.1
  12-b:  77   202-  204 ====  19-b:  A5 A 196-A 199 ! 15.1!  0.1!  3.2
  13-a:   6   223-  236 ....  20-a:  11 A 210-A 218 ! 32.5!  1.7!  7.4
  14-b:  88   243-  246 ====  21-b:  A6 A 219-A 221 ! 19.2!  0.4!  2.5
  15-a:   7   248-  257 .==.  22-a:  12 A 222-A 236 !  8.3!  0.2!  3.7
  16-a:   8   275-  278  ..   22-a:  12 A 222-A 236 !117.2!  1.4! 16.5
  17-b:  99   283-  286 ====  26-b:  A7 A 256-A 258 !  8.4!  0.3!  3.1
  18-a:   9   306-  315  ..   28-a:  17 A 277-A 280 !121.3!  2.3! 15.3
  19-b: 100   319-  323 ====  30-b:  A8 A 298-A 303 !  5.2!  0.2!  2.3
  21-a:  11   333-  345 ====  34-a:  20 A 339-A 352 !  8.9!  1.1!  2.2
  22-b: 111   354-  360  ..   35-b:  E1 A 359-A 363 !  5.2!  5.0!  6.4
  23-b: 122   363-  368 ====  36-b:  E2 A 368-A 372 !  5.6!  1.2!  3.9
 ---------------------------------------------------+-----+-----+------
 Mean Angle:      8.4    Mean Distance:   0.5    RMS:     2.9
 Max Anlge:      19.2    Max Distance:    1.2
 SS match # 15  topological diversity  12.9  in match  1 of mol2
 ----------------------------------------------------------------------
 MATRIX
    -0.9771525     0.1865913    -0.1017673
    -0.0017690     0.4716600     0.8817787
     0.2125318     0.8618124    -0.4605537
 TRANSLATION
    43.7862167     2.5859852     0.1444044
 O_Matrix name: .LSQ_RT_MOL2   
 ----------------------------------------------------------------------
 begin end     Sequence Matching
 ----------------------------------------------------------------------
  3    7       VLFQG                                             
  A4   A8      TFVHL                                             

  20   28      YNMMMGKVD                                         
  A13  A21     WQDVAQECE                                         

  29   47      DIAAAGVTHVWLPPPSHSV                               
  A23  A41     YLGPKGYAAVQVSPPNEHI                               
                    |   |   ||                                   

  54   57      PGRL                                              
  A52  A55     PVSY                                              
               |                                                 

  59   61      DID                                               
  A56  A58     ELQ                                               

  63   95      SKYGNAAELKSLIGALHGKGVQAIADIVINHRC                 
  A59  A91     SRGGNRAQFIDMVNRCSAAGVDIYVDTLINHMA                 
               |  || |            ||    |  |||                   

  106  108     CIF                                               
  A106 A108    KSF                                               
                 |                                               

  119  126     WGPHMICR                                          
  A111 A118    YSPQDFHE                                          
                 |                                               

  147  159     APDIDHLNDRVQR                                     
  A142 A154    LADLDTASNYVQN                                     
                 | |     ||                                      

  161  170     LKEWLLWLKS                                        
  A156 A165    IAAYINDLQA                                        
                      |                                          

  173  194     GFDAWRLDFARGYSPEMAKVYI                            
  A167 A188    GVKGFRFDASKHVAASDIQSLM                            
               |    | |                                          

  201  208     LAVAEVWD                                          
  A196 A203    VVFQEVID                                          
                   || |                                          

  243  259     GMVFDFTTKGILNAAVE                                 
  A218 A234    GLVTEFKYSTELGNTFR                                 
               | |  |     |                                      

  280  293     PAKAVTFVDNHDTG                                    
  A253 A266    SSSAVVFVDNHDNQ                                    
                  || ||||||                                      

  305  318     KVMQGYAYILTHPG                                    
  A283 A296    LYDLANVFMLAYPY                                    
                        |  |                                     

  318  323     GIPCIF                                            
  A297 A302    GYPKVM                                            
               | |                                               

  334  347     DQIAALVAIRKRNG                                    
  A340 A353    SYIAGGVDFRNNTA                                    
                 ||  |  |                                        

 ----------------------------------------------------------------------
 Matching residues 202   Identical residues  48   Identity       23.8%
 Match Rate(1)   15.9%   r.m.s. of atoms   1.37   Mean distance   1.22
 structure diversity  54.01    with  202 residues in match 1 of mol2
 Superimposed coordinates of this match: mol2_mol1.pdb_1  


 ----------------------------------------------------------------------
  14 of ( 26, 42) secondary structure could be aligned.
 ---------------------------------------------------+-----+-----+------
  Nr.E  Mol1 start  endmatch Nr.E  Mol2 start  end !angle! dst ! r.m.s
 ---------------------------------------------------+-----+-----+------
   1-b:  11     4-    6 ====   1-b:  A1 A   5-A   8 ! 12.8!  0.5!  2.3
   2-a:   1    19-   24 .==.   2-a:   1 A  12-A  23 ! 16.0!  1.1!  7.5
   3-a:   2    27-   32 ....   2-a:   1 A  12-A  23 ! 43.0!  1.0!  9.1
   4-b:  22    37-   40 ====   4-b:  A2 A  31-A  34 !  3.7!  0.6!  0.9
   5-a:   3    68-   80 ====   6-a:   4 A  63-A  77 !  3.3!  0.2!  2.4
   6-b:  33    84-   89 ====   7-b:  A3 A  80-A  86 !  3.4!  0.1!  2.3
   7-b:  44    98-   99  ..    8-b:  B1 A  89-A  90 !100.1!  4.8! 14.6
   8-b:  55   105-  107  ..    8-b:  B1 A  89-A  90 ! 95.6!  9.5! 11.8
  10-b:  66   176-  179 ====  16-b:  A4 A 170-A 174 ! 11.0!  0.0!  2.0
  11-a:   5   187-  197 ====  18-a:  10 A 180-A 190 !  3.8!  1.1!  3.0
  12-b:  77   202-  204 ====  19-b:  A5 A 196-A 199 ! 16.9!  0.3!  3.5
  13-a:   6   223-  236 ....  20-a:  11 A 210-A 218 ! 34.3!  1.8!  7.8
  14-b:  88   243-  246 ====  21-b:  A6 A 219-A 221 ! 20.5!  0.5!  2.5
  15-a:   7   248-  257 .==.  22-a:  12 A 222-A 236 !  8.4!  0.4!  3.7
  16-a:   8   275-  278  ..   22-a:  12 A 222-A 236 !118.2!  0.9! 16.5
  17-b:  99   283-  286 ====  26-b:  A7 A 256-A 258 !  8.8!  0.6!  3.5
  18-a:   9   306-  315  ..   28-a:  17 A 277-A 280 !122.0!  1.7! 15.3
  19-b: 100   319-  323 ====  30-b:  A8 A 298-A 303 !  6.2!  0.1!  2.2
  21-a:  11   333-  345 ====  34-a:  20 A 339-A 352 !  8.2!  1.6!  2.7
  22-b: 111   354-  360 ....  35-b:  E1 A 359-A 363 !  6.6!  3.2!  5.5
  23-b: 122   363-  368 ====  36-b:  E2 A 368-A 372 !  7.2!  0.5!  3.2
  24-b: 133   372-  376 ====  37-b:  E3 A 377-A 382 ! 13.5!  1.4!  3.5
  25-b: 144   391-  396  ..   39-b:  G1 A 399-A 402 ! 17.0!  4.2! 10.0
  26-b: 155   399-  403 ====  42-b:  E4 A 437-A 442 ! 18.3!  1.6!  3.5
 ---------------------------------------------------+-----+-----+------
 Mean Angle:      9.8    Mean Distance:   0.7    RMS:     3.0
 Max Anlge:      20.5    Max Distance:    1.6
 SS match # 16  topological diversity  13.3  in match  2 of mol2
 ----------------------------------------------------------------------
 MATRIX
    -0.9771512     0.1867628    -0.1014660
    -0.0013534     0.4719073     0.8816472
     0.2125414     0.8616399    -0.4608719
 TRANSLATION
    43.7637787     2.5735645     0.1539354
 O_Matrix name: .LSQ_RT_MOL22  
 ----------------------------------------------------------------------
 begin end     Sequence Matching
 ----------------------------------------------------------------------
  3    7       VLFQG                                             
  A4   A8      TFVHL                                             

  20   28      YNMMMGKVD                                         
  A13  A21     WQDVAQECE                                         

  29   47      DIAAAGVTHVWLPPPSHSV                               
  A23  A41     YLGPKGYAAVQVSPPNEHI                               
                    |   |   ||                                   

  54   57      PGRL                                              
  A52  A55     PVSY                                              
               |                                                 

  59   61      DID                                               
  A56  A58     ELQ                                               

  63   95      SKYGNAAELKSLIGALHGKGVQAIADIVINHRC                 
  A59  A91     SRGGNRAQFIDMVNRCSAAGVDIYVDTLINHMA                 
               |  || |            ||    |  |||                   

  106  108     CIF                                               
  A106 A108    KSF                                               
                 |                                               

  119  126     WGPHMICR                                          
  A111 A118    YSPQDFHE                                          
                 |                                               

  147  159     APDIDHLNDRVQR                                     
  A142 A154    LADLDTASNYVQN                                     
                 | |     ||                                      

  161  170     LKEWLLWLKS                                        
  A156 A165    IAAYINDLQA                                        
                      |                                          

  173  193     GFDAWRLDFARGYSPEMAKVY                             
  A167 A187    GVKGFRFDASKHVAASDIQSL                             
               |    | |                                          

  201  208     LAVAEVWD                                          
  A196 A203    VVFQEVID                                          
                   || |                                          

  243  259     GMVFDFTTKGILNAAVE                                 
  A218 A234    GLVTEFKYSTELGNTFR                                 
               | |  |     |                                      

  280  293     PAKAVTFVDNHDTG                                    
  A253 A266    SSSAVVFVDNHDNQ                                    
                  || ||||||                                      

  305  318     KVMQGYAYILTHPG                                    
  A283 A296    LYDLANVFMLAYPY                                    
                        |  |                                     

  318  323     GIPCIF                                            
  A297 A302    GYPKVM                                            
               | |                                               

  334  347     DQIAALVAIRKRNG                                    
  A340 A353    SYIAGGVDFRNNTA                                    
                 ||  |  |                                        

 ----------------------------------------------------------------------
 Matching residues 201   Identical residues  48   Identity       23.9%
 Match Rate(1)   15.9%   r.m.s. of atoms   1.35   Mean distance   1.21
 structure diversity  53.91    with  201 residues in match 2 of mol2
 Superimposed coordinates of this match: mol2_mol1.pdb_2  


 ----------------------------------------------------------------------
  13 of ( 26, 42) secondary structure could be aligned.
 ---------------------------------------------------+-----+-----+------
  Nr.E  Mol1 start  endmatch Nr.E  Mol2 start  end !angle! dst ! r.m.s
 ---------------------------------------------------+-----+-----+------
   3-a:   2    27-   32 ====   3-a:   2 A  23-A  28 ! 10.1!  0.2!  3.8
   4-b:  22    37-   40 ====   4-b:  A2 A  31-A  34 !  3.8!  0.7!  0.9
   5-a:   3    68-   80 ====   6-a:   4 A  63-A  77 !  3.2!  0.3!  2.2
   6-b:  33    84-   89 ====   7-b:  A3 A  80-A  86 !  3.5!  0.3!  2.5
   7-b:  44    98-   99  ..    8-b:  B1 A  89-A  90 !100.0!  4.9! 14.2
   8-b:  55   105-  107  ..    8-b:  B1 A  89-A  90 ! 95.8!  9.3! 11.5
  10-b:  66   176-  179 ====  16-b:  A4 A 170-A 174 ! 10.9!  0.1!  2.2
  11-a:   5   187-  197 ====  18-a:  10 A 180-A 190 !  3.7!  0.9!  3.2
  12-b:  77   202-  204 ====  19-b:  A5 A 196-A 199 ! 17.0!  0.0!  3.3
  13-a:   6   223-  236 ....  20-a:  11 A 210-A 218 ! 34.5!  2.1!  7.9
  14-b:  88   243-  246 ====  21-b:  A6 A 219-A 221 ! 20.5!  0.4!  2.6
  15-a:   7   248-  257 .==.  22-a:  12 A 222-A 236 !  8.6!  0.7!  3.7
  16-a:   8   275-  278  ..   22-a:  12 A 222-A 236 !118.0!  0.8! 16.6
  17-b:  99   283-  286 ====  26-b:  A7 A 256-A 258 !  9.0!  0.8!  3.4
  18-a:   9   306-  315  ..   28-a:  17 A 277-A 280 !122.0!  1.5! 15.6
  19-b: 100   319-  323 ====  30-b:  A8 A 298-A 303 !  6.2!  0.1!  2.4
  22-b: 111   354-  360  ..   31-b:  D1 A 321-A 322 ! 63.0!  1.1! 43.0
  23-b: 122   363-  368 ====  36-b:  E2 A 368-A 372 !  7.2!  0.4!  3.0
  24-b: 133   372-  376 ====  37-b:  E3 A 377-A 382 ! 13.5!  1.4!  3.4
  25-b: 144   391-  396  ..   39-b:  G1 A 399-A 402 ! 16.8!  4.1!  9.6
  26-b: 155   399-  403 ====  42-b:  E4 A 437-A 442 ! 18.3!  1.6!  3.6
 ---------------------------------------------------+-----+-----+------
 Mean Angle:      9.8    Mean Distance:   0.6    RMS:     3.1
 Max Anlge:      20.5    Max Distance:    1.6
 SS match # 14  topological diversity  16.3  in match  3 of mol2
 ----------------------------------------------------------------------
 MATRIX
    -0.9771512     0.1867628    -0.1014660
    -0.0013534     0.4719073     0.8816472
     0.2125414     0.8616399    -0.4608719
 TRANSLATION
    43.7637787     2.5735645     0.1539354
 O_Matrix name: .LSQ_RT_MOL23  
 ----------------------------------------------------------------------
 begin end     Sequence Matching
 ----------------------------------------------------------------------
  3    7       VLFQG                                             
  A4   A8      TFVHL                                             

  20   28      YNMMMGKVD                                         
  A13  A21     WQDVAQECE                                         

  29   47      DIAAAGVTHVWLPPPSHSV                               
  A23  A41     YLGPKGYAAVQVSPPNEHI                               
                    |   |   ||                                   

  54   57      PGRL                                              
  A52  A55     PVSY                                              
               |                                                 

  59   61      DID                                               
  A56  A58     ELQ                                               

  63   95      SKYGNAAELKSLIGALHGKGVQAIADIVINHRC                 
  A59  A91     SRGGNRAQFIDMVNRCSAAGVDIYVDTLINHMA                 
               |  || |            ||    |  |||                   

  106  108     CIF                                               
  A106 A108    KSF                                               
                 |                                               

  119  126     WGPHMICR                                          
  A111 A118    YSPQDFHE                                          
                 |                                               

  147  159     APDIDHLNDRVQR                                     
  A142 A154    LADLDTASNYVQN                                     
                 | |     ||                                      

  161  170     LKEWLLWLKS                                        
  A156 A165    IAAYINDLQA                                        
                      |                                          

  173  193     GFDAWRLDFARGYSPEMAKVY                             
  A167 A187    GVKGFRFDASKHVAASDIQSL                             
               |    | |                                          

  201  208     LAVAEVWD                                          
  A196 A203    VVFQEVID                                          
                   || |                                          

  243  259     GMVFDFTTKGILNAAVE                                 
  A218 A234    GLVTEFKYSTELGNTFR                                 
               | |  |     |                                      

  280  293     PAKAVTFVDNHDTG                                    
  A253 A266    SSSAVVFVDNHDNQ                                    
                  || ||||||                                      

  305  318     KVMQGYAYILTHPG                                    
  A283 A296    LYDLANVFMLAYPY                                    
                        |  |                                     

  318  323     GIPCIF                                            
  A297 A302    GYPKVM                                            
               | |                                               

  334  347     DQIAALVAIRKRNG                                    
  A340 A353    SYIAGGVDFRNNTA                                    
                 ||  |  |                                        

 ----------------------------------------------------------------------
 Matching residues 201   Identical residues  48   Identity       23.9%
 Match Rate(1)   15.9%   r.m.s. of atoms   1.35   Mean distance   1.21
 structure diversity  53.91    with  201 residues in match 3 of mol2
 Superimposed coordinates of this match: mol2_mol1.pdb_3  


 <<mol1.pdb  Max Align: 14  Max Match: 16
 Best Topological Diversity  12.9  with 15 matched SS to  mol2
 Best Structure Diversity   53.91 with  201 matched residues to mol2
 Superimposed Model with least SD: mol2_mol1.pdb

 #Ca 201 RMS: 1.4 dist. 1.2 str.div:  53.9 top.div  12.9
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


CPU time:   7.0 sec


The superimposed coordinates from Mol2 to Mol1 are listed in following
Superimposed model with lesat structure diversity
Superimposed structure in each match

1 2